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=== - File formats (E) === || '''Format''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || FASTA |||| File format for representing biological sequences |||| [[http://blast.ncbi.nlm.nih.gov/blastcgihelp.shtml|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/3162770|PubMed]] || || GFF3 |||| File format for representing gene annotations |||| [[http://www.sequenceontology.org/gff3.shtml|Link]] |||| -- || || BioPax |||| Pathway exchange language for Biological pathway data |||| [[http://www.biopax.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/20829833|PubMed]] || || Extended Newick |||| Standard for representation of phylogenetic networks |||| [[http://dmi.uib.es/~gcardona/BioInfo/enewick.html|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/19077301|PubMed]] || === - Biological libraries of programming languages (E) === || '''Library''' |||| '''Description''' |||| '''URl''' |||| '''Reference''' || || BioJava |||| Open source project for Java tools for bioinformatics |||| [[http://www.biojava.org|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/22877863|PubMed]] || || BioPerl |||| Collection of Perl modules for bioinformatics applications |||| [[http://www.bioperl.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/12368254|PubMed]] || || BioPython |||| Open source collection of Python tools for bioinformatics |||| [[http://www.biopython.org|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/19304878|PubMed]] || || BioJS |||| Full-featured biological workbench written in JS |||| [[http://www.ebi.ac.uk/tools/biojs/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/25075290|PubMed]] || || R Bioconductor |||| Collection of R packages provides tools for the analysis biological data |||| [[http://www.bioconductor.org/|Link]] |||| [[http://www.ncbi.nlm.nih.gov/pubmed/15461798|PubMed]] || |
Ten Simple Rules for Developing Public Biological Databases
Supplementary Webpage for Tools and Technologies Recommendations
R: Recommendation, E: Example
- Resources for available databases (R)
Resource |
Description |
URl |
Reference |
|||
NAR 2016's Database Collection |
NAR collection of online Molecular Biology Database 2016 |
|||||
Pathguide |
The Pathway Resource List |
|||||
The Registry |
Collection of analytical tools and data services for bioinformatics |
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The Bioinformatics Links Directory |
List of curated links to molecular resources, tools and databases |
|||||
OMICtools |
Collection of classified omic tools |
|||||
A user-contributed database of biological databases |
||||||
- Ontologies and semantics (R)
- File formats (E)
Format |
Description |
URl |
Reference |
|||
FASTA |
File format for representing biological sequences |
|||||
GFF3 |
File format for representing gene annotations |
-- |
||||
Pathway exchange language for Biological pathway data |
||||||
Extended Newick |
Standard for representation of phylogenetic networks |
|||||
- Biological libraries of programming languages (E)
Library |
Description |
URl |
Reference |
|||
Open source project for Java tools for bioinformatics |
||||||
Collection of Perl modules for bioinformatics applications |
||||||
Open source collection of Python tools for bioinformatics |
||||||
BioJS |
Full-featured biological workbench written in JS |
|||||
R Bioconductor |
Collection of R packages provides tools for the analysis biological data |
|||||